I disagree. As you say the circumstances in the region are out of the ordinary and there is a degree of uncertainty as to what will happen. The new Egypt have been increasingly assertive in it's foreign policy as opposed to pre-revolutionary Egypt which was essentially an american puppet state. So the reality is that Egypt is looking to safeguard it's own national interest in the region for the first time. In order to do so it needs to recognize the major players in the region and interact with them to decrease the level of uncertainty and shift the circumstances as close to Egypts interests as possible. Of course Iran is one of these major players and I think Morsi signaled that he recognized this to Iran and the world when he just recently invited it to a quartet with the aim of negotiating a solution in Syria. He is basically saying that the region cannot ignore the elephant standing in the room and so it follows that Egypt should have relations with Iran in order to safeguard it's interests in the region. Interestingly USA was not invited to this group which is consistent with my point of a new assertive Egypt.
On a lesser note I should comment on your assertion that Egypt needs to take Iran's standing in the sunni states into consideration and point out that if you flip the coin you have a situation where Egypt needs to analyze Iran's standing in the Shia states of the region and what this means for Egypt.
There is no reason why Egypt and Iran should not have diplomatic ties when Saudi Arabia and Iran can maintain the ties despite hostilities and divergence on many issues. Have you seen the Pics of Ahamdinejad sitting right to King Abdullah in the recently concluded OIC extra ordinary session on Syria in the KSA?. I raised two points that who gets what in the present geopolitics of Middle East, its Iran who is more willing to resume the ties and it is evident why they are. You rightly said that after regime change Egypt is taking back its leadership position in MENA region. If you carefully study the moves and statements of Morsi he would like to take along Iran rather than get along with Iran especially on the issue of Syria ( watch his address in NAM summit recently concluded in Tehran).
As far as your point on flip side (Iran’s standing in Shiet states ), there is not much scope for maneuvering apart from Iran there are Azerbaijan ( that is more close to Turkey), Iraq and Hezbollah of Lebanon and these two are directly linked with the issue of Syria that is on high priority of Morsi.
I always wondered , does Egypt get money from ships passing suez canal and if so how much , because everytime i look at the map its such an important place .
In 2011 they have earned around 4.5 billion USD in transit fees this year they expect around 5 Billion USD. this is realy huge sum....